Pablo Riesgo-Ferreiro

Python version needs to be changed to 3.9

ping @RJMW, @ludwigc

Agreed with @johausmann to add subworkfows to alleviate the issue with ifs in `main.nf`

Just added in #37 the FASTA sequences to the output. Will follow up on the rest, the filtering by depth requires a thorough analysis from our side. The whole dataset...

Apologies for ultra-late response @Rohit-Satyam , we have not looked into this yet. We will eventually get here. FYI @johausmann

Three options at least: - Escape white spaces with something like under scores - Escape white spaces with HTML codes and expect that IGV&friends parse this properly - Integrate pfam...

Fourth option: remove the Pfam long description altogether if not used in the dashboard

Thanks for your feedback @corneliusroemer , it is a nice compliment coming from someone working in Nextclade! The QC metrics are very interesting, we will need to understand more of...

I suspect for the tests to pass, you may need to merge the latest merged PR from master into this branch, as it updated to Java 11.

It would be a good moment to update all GATK dependencies. Also, if I remember right, there were two similar, but still different GATK versions.